In MySQLConnection::connection() we propagate the config options for truststore/keystore to JVM-level system properties:

setSystemProperty("javax.net.ssl.keyStore", MySqlConnectorConfig.SSL_KEYSTORE, true);
setSystemProperty("javax.net.ssl.keyStorePassword", MySqlConnectorConfig.SSL_KEYSTORE_PASSWORD, false);
setSystemProperty("javax.net.ssl.trustStore",MySqlConnectorConfig.SSL_TRUSTSTORE, true);
setSystemProperty("javax.net.ssl.trustStorePassword", MySqlConnectorConfig.SSL_TRUSTSTORE_PASSWORD, false);

As of Connector/J 8.0, this should not be needed, as those options can be set solely at a connector level, i.e. we should propagate them in the "database." connector property namespace, using the names given in the driver docs. This will allow to use multiple connectors with different truststore/keystore settings on a single JVM.